>>21970702It works just like arranging your boxes on the in-game PC, just with a second "PC" that you can move them to. Also, IIRC you can't move any Pokemon that are currently in your party, just the boxed ones.
If you have two physical copies then you just start the app up with Y in your 3DS, move the Pokemon you want in Ruby to the Pokebank boxes, then exit, put in Ruby, start it up again and move the Pokemon from the Pokebank boxes to your boxes in Ruby.
You'll need to have gotten the Pokedex in the game for it to let you transfer anything to Ruby, so you'll have to play for just a little bit before you can move anything over. Also it has a $5 annual fee that you have to pay before you can use it.
